EP 3587586 A1 20200101 - METHOD FOR STATISTICALLY DETERMINING A QUANTIFICATION OF OLD AND NEW RNA
Title (en)
METHOD FOR STATISTICALLY DETERMINING A QUANTIFICATION OF OLD AND NEW RNA
Title (de)
VERFAHREN ZUR STATISTISCHEN BESTIMMUNG EINER QUANTIFIZIERUNG VON ALTER UND NEUER RNA
Title (fr)
PROCÉDÉ POUR STATISTIQUEMENT DÉTERMINER UNE QUANTIFICATION DE NOUVEAU ET D'ANCIEN ARN
Publication
Application
Priority
EP 18179371 A 20180622
Abstract (en)
The present invention provides a method for determining a quantification of old and new RNA for a gene, the method comprising:- obtaining reads from RNA fragments of a sample, wherein the RNA fragments comprise nucleotide substitutions caused by a metabolic marker,- determining statistics of nucleotide mismatches in the reads,- determining, based on the statistics of nucleotide mismatches, an error rate indicating a rate of nucleotide mismatches in old RNA and a conversion rate indicating a rate of nucleotide mismatches in new RNA, and- determining the quantification of old and newly synthesized RNA for the gene based on the error rate, the conversion rate and the statistics for the gene.
IPC 8 full level
C12Q 1/68 (2018.01); C12Q 1/6869 (2018.01)
CPC (source: EP US)
C12Q 1/6869 (2013.01 - EP US); G16B 30/00 (2019.01 - EP US)
Citation (search report)
- [I] HERZOG VERONIKA A ET AL: "Thiol-linked alkylation of RNA to assess expression dynamics", NATURE METHODS, NATURE PUBLISHING GROUP, GB, 25 September 2017 (2017-09-25), XP009500433, ISSN: 1548-7105, DOI: 10.1038/NMETH.4435 & VERONIKA A HERZOG ET AL: "Thiol-linked alkylation of RNA to assess expression dynamics", NATURE METHODS, vol. 14, no. 12, 25 September 2017 (2017-09-25), New York, pages 1198 - 1204, XP055502021, ISSN: 1548-7091, DOI: 10.1038/nmeth.4435
- [I] MARISA BAPTISTA ET AL: "RNA dynamics revealed by metabolic RNA labeling and biochemical nucleoside conversions", NATURE METHODS, 28 February 2018 (2018-02-28), United States, pages 171 - 172, XP055500889, Retrieved from the Internet <URL:https://www.nature.com/articles/nmeth.4608.pdf> [retrieved on 20180824], DOI: 10.1038/nmeth.4608
- [I] BERND RÄDLE ET AL: "Metabolic Labeling of Newly Transcribed RNA for High Resolution Gene Expression Profiling of RNA Synthesis, Processing and Decay in Cell Culture", JOURNAL OF VISUALIZED EXPERIMENTS, no. 78, 8 August 2013 (2013-08-08), XP055501988, DOI: 10.3791/50195
- [I] WAYO MATSUSHIMA ET AL: "SLAM-ITseq: Sequencing cell type-specific transcriptomes without cell sorting", BIORXIV, 16 December 2017 (2017-12-16), XP055502086, Retrieved from the Internet <URL:https://www.biorxiv.org/content/biorxiv/early/2017/12/16/235093.full.pdf> [retrieved on 20180824], DOI: 10.1101/235093
- [A] C. MILLER ET AL: "Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast", MOLECULAR SYSTEMS BIOLOGY, vol. 7, no. 1, 16 April 2014 (2014-04-16), pages 458 - 458, XP055500892, DOI: 10.1038/msb.2010.112
- [A] CAROLINE C. FRIEDEL ET AL: "Conserved principles of mammalian transcriptional regulation revealed by RNA half-life", NUCLEIC ACIDS RESEARCH, vol. 37, no. 17, 26 June 2009 (2009-06-26), pages e115 - e115, XP055500894, ISSN: 0305-1048, DOI: 10.1093/nar/gkp542
- [A] ALEXANDER DOBIN ET AL: "STAR: ultrafast universal RNA-seq aligner", BIOINFORMATICS., vol. 29, no. 1, 25 October 2012 (2012-10-25), GB, pages 15 - 21, XP055500895, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/bts635
Designated contracting state (EPC)
AL AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO PL PT RO RS SE SI SK SM TR
Designated extension state (EPC)
BA ME
DOCDB simple family (publication)
EP 3587586 A1 20200101; EP 3810802 A1 20210428; US 2021272651 A1 20210902; WO 2019242991 A1 20191226
DOCDB simple family (application)
EP 18179371 A 20180622; EP 19725382 A 20190524; EP 2019063543 W 20190524; US 201917255238 A 20190524